An air conditioning system for motor vehicles includes an air conditioner case having a left path, a right path and a rear seat path. A temperature door is configured to adjust a volume of a cold air or a hot air. A main blower is configured to blow the cold air or the hot air and an air volume distribution door is configured to control opening degrees of the left path and the right path. A rear seat auxiliary blower is configured to increase a volume and a pressure of the cold air or the hot air flowing through the rear seat path. A control unit is configured to, when an air volume distribution ratio of the main blower is changed, correct an opening position of the air volume distribution door and compensate a change in an air volume distribution ratio of the left path and the right path.